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There is probably something wrong with the DOCTYPE, a space where it doesn't mean to be or something of that order.
There is a selection in preferences for pretty print or Tidy at open or save which you can turn on to import flawed files, and then turn back off after you have brought them in.
The DOCTYPE is the same for all epubs, as far as I know, so you can copy the first part of the epub from a valid one and paste it over the problem stuff.
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